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9spc

;Recombinant human butyrylcholinesterase in complex with ethyl 1-[3-(2-oxopyrrolidin-1-yl)propyl]-2-phenyl-1H-1,3-benzodiazole-5-carboxylate ;

Method: X-RAY DIFFRACTION D_max: 78.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9spc
deposition_date	2025-09-16
last_revision	2026-02-18
title	;Recombinant human butyrylcholinesterase in complex with ethyl 1-[3-(2-oxopyrrolidin-1-yl)propyl]-2-phenyl-1H-1,3-benzodiazole-5-carboxylate ;
keywords	Butyrylcholinesterase, Inhibitor, Complex, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	24.25 Å
rg_electron	23.15 Å
i0	120272000.00
molecular_weight	58599.0 kDa
excluded_volume	57028 Å³
envelope_volume	91675 Å³
shell_volume	31549 Å³
envelope_diameter	79.7 Å
shell_rg	31.70 Å
envelope_rg	23.62 Å
shape_rg	23.09 Å
total_rg	23.92 Å
total_atoms	4440
n_residues	526
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	78.8 Å
rg_real	24.09 Å
rg_real_error	0.44 Å
i0_real	1.2030e+08
i0_real_error	1.5940e+06
rg_reciprocal	24.13 Å
i0_reciprocal	120300000.0000
total_estimate	0.8866
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	77.6 Å
skewness	0.184
kurtosis	-0.400
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	33890000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Cholinesterase
formula_weight	59713.5 kDa
ec_number	3.1.1.8
mutation	;N17Q, N455Q, N481Q, N486Q engineered mutations to prevent excessive N-glycosylation. Numeration on the mature enzyme, without the signal peptide. ;
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4612

EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	2

Entity 4 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	ethyl 1-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]-2-phenyl-benzimidazole-5-carboxylate
formula_weight	391.5 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	N-acetyl-alpha-neuraminic acid
formula_weight	309.3 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	130

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6. Citations (1)

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length_a	154.134 Å
length_b	154.134 Å
length_c	128.387 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	tetragonal

resolution	2.660 Å
resolution_low	48.740 Å
r_factor	0.1826
r_work	0.1797
r_free	0.2396

fit	/app/data/saxs_computation/sp/9spc/9spc.fit
pddf	/app/data/pr_computation/sp/9spc/9spc.pr.out
profile	/app/data/saxs_computation/sp/9spc/9spc.dat